Apparent Bio-formats error

[Joel Sheffield]

THis may have come up before, but... We are still working with the Leica
.lei file system, in which the individual images are stored as simple tifs,
and there is an extensive .lei file that defines the characteristics of the
confocal series.  We have discovered that although we can easily open files
with my old 32-bit PC, we get two kinds of error with a 64-bit pc.  Both
are running Win7.  The error takes the following form:
Either.

1.after the opening screen, there is a message like "reading header" in the
ImageJ menu, and then nothing happens.  The system is not frozen, but there
is no progress either.

2. Sometimes, we also get the following error message



We've tried to return to the earlier versions of Bioformats, but that
doesn't work either.  Any ideas of what might be going wrong?


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

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[ctrueden]

Hi Joel,

> The system is not frozen, but there is no progress either.

If you run ImageJ from the Command Prompt with "ImageJ-win64.exe --console"
(IIRC), you can then press Ctrl+Pause at any time to get a stack trace.
This may shed light on how the file import is hanging.

Your error message didn't come through. The space after your #2 list item
is just blank.

> We've tried to return to the earlier versions of Bioformats, but that
> doesn't work either.

Doesn't work how? Same error? Different error?

You might want to send this bug report to the OME mailing list [1].

Regards,
Curtis

[1]
https://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html


On Fri, May 23, 2014 at 10:50 PM, JOEL B. SHEFFIELD <[hidden email]> wrote:

> THis may have come up before, but... We are still working with the Leica
> .lei file system, in which the individual images are stored as simple tifs,
> and there is an extensive .lei file that defines the characteristics of the
> confocal series.  We have discovered that although we can easily open files
> with my old 32-bit PC, we get two kinds of error with a 64-bit pc.  Both
> are running Win7.  The error takes the following form:
> Either.
>
> 1.after the opening screen, there is a message like "reading header" in the
> ImageJ menu, and then nothing happens.  The system is not frozen, but there
> is no progress either.
>
> 2. Sometimes, we also get the following error message
>
>
>
> We've tried to return to the earlier versions of Bioformats, but that
> doesn't work either.  Any ideas of what might be going wrong?
>
>
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: [hidden email]
> URL:  http://astro.temple.edu/~jbs
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi,

On Mon, 26 May 2014, Curtis Rueden wrote:

> > The system is not frozen, but there is no progress either.
>
> If you run ImageJ from the Command Prompt with "ImageJ-win64.exe --console"
> (IIRC), you can then press Ctrl+Pause at any time to get a stack trace.

It is not too uncommon that problems have to be diagnosed via the
command-line, so I started documenting that procedure here:
http://fiji.sc/Command-Line_Debugging.

Ciao,
Johannes

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[Thomas GUILBERT]

Dear all,

I used to work on my old computer with "large" NDPI files from Hamamatsu
Nanozoomer acquisitions.
To treat this kind of large files, I use NDPI tools plugin :
- PreviewNDPI
- Selection of small ROI (I asume entire image too big)
- Extract to TIFF
- then, my processing.

Selection of ROIs is time consuming.
I actually use new 64bits Win7 32GbRAM 3GbRAM Graphic Card's computer.
Well, if I want to convert an _entire NDPI image_ to tiff (full
resolution), I only get this error message : "Illegal page requested
from a TIFF file."

I tried to open it with LOCI, full resolution (46080*41728, 3 planes), I
got
"java.lang.ArrayIndexOutOfBoundsException: 1473511424" error.
The 11520*10432 resolution open, but the quality is not here.

Could anyone tell me what are the limits ?

Thanks all,

--
Thomas GUILBERT, PhD
Plate-Forme Cochin Imagerie,
Institut Cochin - INSERM U1016
Bât. Gustave Roussy 5ème étage
22 rue Méchain, 75014 PARIS
 
tel: [phone]

http://www.cochin.inserm.fr/
[hidden email]  


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[ctrueden]

Hi Thomas,

> I tried to open it with LOCI, full resolution (46080*41728, 3 planes),
> I got "java.lang.ArrayIndexOutOfBoundsException: 1473511424" error.
> The 11520*10432 resolution open, but the quality is not here.

If you crop your image (using the "Crop on import" checkbox) such that the
opened plane is less than 2 gigapixels in size (width times height),
Bio-Formats should be open the full resolution data one tile at a time.

You could also try converting to TIFF in one shot using the Bio-Formats
command line tools [1] ("bfconvert" command), though I have not tested this
with image planes exceeding 2 GPix.

Regards,
Curtis

[1]
https://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/


On Wed, May 28, 2014 at 2:16 AM, Thomas GUILBERT
<[hidden email]>wrote:

> Dear all,
>
> I used to work on my old computer with "large" NDPI files from Hamamatsu
> Nanozoomer acquisitions.
> To treat this kind of large files, I use NDPI tools plugin :
> - PreviewNDPI
> - Selection of small ROI (I asume entire image too big)
> - Extract to TIFF
> - then, my processing.
>
> Selection of ROIs is time consuming.
> I actually use new 64bits Win7 32GbRAM 3GbRAM Graphic Card's computer.
> Well, if I want to convert an _entire NDPI image_ to tiff (full
> resolution), I only get this error message : "Illegal page requested from a
> TIFF file."
>
> I tried to open it with LOCI, full resolution (46080*41728, 3 planes), I
> got
> "java.lang.ArrayIndexOutOfBoundsException: 1473511424" error.
> The 11520*10432 resolution open, but the quality is not here.
>
> Could anyone tell me what are the limits ?
>
> Thanks all,
>
> --
> Thomas GUILBERT, PhD
> Plate-Forme Cochin Imagerie,
> Institut Cochin - INSERM U1016
> Bât. Gustave Roussy 5ème étage
> 22 rue Méchain, 75014 PARIS
>  tel: [phone]
>
> http://www.cochin.inserm.fr/
> [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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